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Twist and induce: Dissecting the link between the enzymatic activity and the SaPI inducing capacity of the phage 80 dUTPase. D95E mutant from dUTPase 80alpha phage.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 20% Ethanol; 10% Glicerol
Crystal Properties Matthews coefficient Solvent content 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.27 α = 90 b = 87.27 β = 90 c = 87.27 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2016-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97921 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 87.27 100 0.038 0.898 15.4 18 7924
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 100 0.573 0.658 2 18.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ZEZ 2.5 61.71 7533 374 100 0.22853 0.22569 0.2266 0.28055 0.2721 RANDOM 60.162
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_4_deg 16.01 r_dihedral_angle_3_deg 13.026 r_dihedral_angle_1_deg 5.873 r_long_range_B_refined 5.461 r_long_range_B_other 5.33 r_mcangle_it 3.153 r_mcangle_other 3.151 r_scangle_other 2.879 r_mcbond_it 1.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_4_deg 16.01 r_dihedral_angle_3_deg 13.026 r_dihedral_angle_1_deg 5.873 r_long_range_B_refined 5.461 r_long_range_B_other 5.33 r_mcangle_it 3.153 r_mcangle_other 3.151 r_scangle_other 2.879 r_mcbond_it 1.809 r_mcbond_other 1.808 r_scbond_other 1.631 r_scbond_it 1.629 r_angle_refined_deg 1.14 r_angle_other_deg 0.823 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1299 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing